Downloaded a book onto it wirelessly via amazon to check it out, all was good.

Hooked up to pc, calibre recognized it. I was able to pick books and send them to the paperwhite.

Ejected the kindle, took it out of sleep, and none of the books showed up. Not only did the books i tried to load from calibre not show up, also the book i downloaded from amazon and the stuff that came on it (dictionaries, etc) disappeared as well!

eep.

Hooked it back up to my pc, and browsed the kindle filesystem. Everything appears to be there in the /document directory, even the missing book and dictionaries.

Fired up calibre, the books show as on the device. And they are.

But as far as the kindle is concerned, they don't exist.

Perhaps it has something to do with the subfolders created? Though even if that was the case, why did the included content disappear?

The dictionaries are in a subfolder /documents/dictionaries/dictionary name. The kindle guide and the amazon book are just in /documents. Everything I loaded from calibre went in to author subfolders, such as /documents/Bryson, Bill/book name/

when I hit the debug device detection button, i get:
calibre, version 0.9.0
ERROR: Device already detected: A device (Amazon Kindle) is already detected by calibre. If you wish to debug the detection of another device, first disconnect this device.

and omg, how much do i LOVE the fact that you have a "copy to clipboard" button on your error box

@markw: Are you saying that the paperwhite accepts only azw3 and not mobi files. That would be extremely silly if it were true. Note that you can control what formats calibre sends to the device by right clicking on the kindle icon in the calibre toolbar and selecting "configure this device"

Ok, so it looks like the paperwhite has the same usb ids as the Kindle 2/3/Touch. That makes it even odder that it seems to work differently than those devices. Can you do the following tests:

0) delete the files you recently sent to the device

1) Right click the kindle icon on the calibre toolbar and select configure this device. Uncheck the option to use sub directories. calibre should then put files directly into the documents folder. See if sending a mobi like that works.

2) Again configure the driver, this time telling it to send the azw3 format instead of mobi. Check if the azw3 file works (both in subdirectories and not in sub directories)

Also are you generating old style mobi or the new "combined" mobi that contains both kf8 and mobi7?

Interesting, played a little bit more with it. I've got a lot of books from Baen, and if I dump them on there in .mobi they don't show up unless I select display all items. Then they show as "personal" I'm wondering if the conversion from mobi -> azw3 removed that setting. So right now most of my .mobi books show up as docs. If you select where it says books(#) and select all items, it will show everything.

Ah so the kindle is recognizing the mobi files. That is good. It seems like the paperwhite firmware has the same kind of separation between "books" and "personal documents" as the kindle fire (one of amazon's sillier ideas).

I'll change the kindle driver in the next release to not put books in sub folders. Amazon seems to have decided they dont like folders, the Kindle Fires and the Kindle for android app all dont support sub-folders either.